Starting phenix.real_space_refine on Tue Jul 29 21:31:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqt_50668/07_2025/9fqt_50668_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqt_50668/07_2025/9fqt_50668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fqt_50668/07_2025/9fqt_50668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqt_50668/07_2025/9fqt_50668.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqt_50668/07_2025/9fqt_50668_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqt_50668/07_2025/9fqt_50668_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 3854 2.51 5 N 936 2.21 5 O 1092 1.98 5 H 5667 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11589 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 8104 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3320 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.35, per 1000 atoms: 0.63 Number of scatterers: 11589 At special positions: 0 Unit cell: (108.9, 80.025, 106.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1092 8.00 N 936 7.00 C 3854 6.00 H 5667 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 73 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 184 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " BETA1-6 " NAG D 1 " - " FUC D 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1001 " - " ASN A 229 " " NAG C 1 " - " ASN A 223 " " NAG D 1 " - " ASN B 12 " " NAG I 1 " - " ASN B 168 " Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 66.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 48 through 61 removed outlier: 3.750A pdb=" N VAL A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLY A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.686A pdb=" N LEU A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 106 through 141 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.687A pdb=" N GLY A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 186 through 212 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 5.838A pdb=" N GLY A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.874A pdb=" N ALA A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 305 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.595A pdb=" N GLY A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.906A pdb=" N ALA A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.848A pdb=" N ILE A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.827A pdb=" N ALA A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 Processing helix chain 'A' and resid 397 through 424 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 482 through 509 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.658A pdb=" N LEU A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.620A pdb=" N ALA B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 127 through 134 removed outlier: 4.489A pdb=" N SER B 132 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.985A pdb=" N GLN B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 199 through 204 removed outlier: 4.130A pdb=" N THR B 202 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 33 removed outlier: 6.718A pdb=" N VAL B 17 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 27 " --> pdb=" O TRP B 15 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP B 15 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 29 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 13 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN B 31 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B 11 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 117 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 167 368 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5656 1.03 - 1.23: 24 1.23 - 1.42: 2527 1.42 - 1.62: 3485 1.62 - 1.82: 56 Bond restraints: 11748 Sorted by residual: bond pdb=" N CYS A 255 " pdb=" CA CYS A 255 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.36e+00 bond pdb=" N THR A 254 " pdb=" H THR A 254 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" N PHE A 259 " pdb=" H PHE A 259 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" N ALA A 258 " pdb=" H ALA A 258 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" N PHE A 256 " pdb=" H PHE A 256 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.45e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 21010 2.32 - 4.64: 141 4.64 - 6.96: 9 6.96 - 9.27: 2 9.27 - 11.59: 2 Bond angle restraints: 21164 Sorted by residual: angle pdb=" CZ TYR A 257 " pdb=" OH TYR A 257 " pdb=" HH TYR A 257 " ideal model delta sigma weight residual 110.00 119.91 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA PRO A 275 " pdb=" N PRO A 275 " pdb=" CD PRO A 275 " ideal model delta sigma weight residual 112.00 107.93 4.07 1.40e+00 5.10e-01 8.47e+00 angle pdb=" CA ALA A 258 " pdb=" C ALA A 258 " pdb=" O ALA A 258 " ideal model delta sigma weight residual 120.42 117.35 3.07 1.06e+00 8.90e-01 8.37e+00 angle pdb=" CA TYR A 257 " pdb=" C TYR A 257 " pdb=" O TYR A 257 " ideal model delta sigma weight residual 120.10 117.18 2.92 1.13e+00 7.83e-01 6.69e+00 angle pdb=" CB MET A 533 " pdb=" CG MET A 533 " pdb=" SD MET A 533 " ideal model delta sigma weight residual 112.70 120.03 -7.33 3.00e+00 1.11e-01 5.96e+00 ... (remaining 21159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.86: 5387 20.86 - 41.72: 271 41.72 - 62.58: 129 62.58 - 83.44: 8 83.44 - 104.29: 6 Dihedral angle restraints: 5801 sinusoidal: 3171 harmonic: 2630 Sorted by residual: dihedral pdb=" CB CYS B 72 " pdb=" SG CYS B 72 " pdb=" SG CYS B 87 " pdb=" CB CYS B 87 " ideal model delta sinusoidal sigma weight residual -86.00 -51.14 -34.86 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual 93.00 124.35 -31.35 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.58 104.29 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 5798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 846 0.057 - 0.114: 128 0.114 - 0.172: 12 0.172 - 0.229: 3 0.229 - 0.286: 1 Chirality restraints: 990 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.68 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 168 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 987 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 274 " -0.088 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO A 275 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 279 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO A 280 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 367 " -0.016 2.00e-02 2.50e+03 1.18e-02 4.16e+00 pdb=" CG PHE A 367 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 367 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 367 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 367 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 367 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 367 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 367 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 367 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 367 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 367 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 367 " -0.001 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 465 2.16 - 2.77: 22086 2.77 - 3.38: 34179 3.38 - 3.99: 42326 3.99 - 4.60: 67156 Nonbonded interactions: 166212 Sorted by model distance: nonbonded pdb=" OE2 GLU A 237 " pdb=" H THR B 95 " model vdw 1.549 2.450 nonbonded pdb="HD22 ASN A 216 " pdb=" O LEU A 303 " model vdw 1.558 2.450 nonbonded pdb=" H GLY A 236 " pdb=" OD2 ASP B 86 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU B 147 " pdb=" H GLU B 147 " model vdw 1.601 2.450 nonbonded pdb=" O LEU A 337 " pdb=" HG SER A 341 " model vdw 1.647 2.450 ... (remaining 166207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6097 Z= 0.189 Angle : 0.688 10.273 8358 Z= 0.346 Chirality : 0.042 0.286 990 Planarity : 0.007 0.132 1016 Dihedral : 13.959 104.295 2296 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.31), residues: 754 helix: 1.32 (0.25), residues: 410 sheet: 0.35 (0.70), residues: 58 loop : 0.45 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 109 HIS 0.005 0.001 HIS B 112 PHE 0.034 0.001 PHE A 367 TYR 0.021 0.001 TYR A 235 ARG 0.005 0.001 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 4) link_NAG-ASN : angle 3.12925 ( 12) link_BETA1-4 : bond 0.01238 ( 4) link_BETA1-4 : angle 3.46825 ( 12) link_ALPHA1-3 : bond 0.00566 ( 1) link_ALPHA1-3 : angle 1.49053 ( 3) hydrogen bonds : bond 0.14500 ( 368) hydrogen bonds : angle 6.37340 ( 1047) link_BETA1-6 : bond 0.00424 ( 1) link_BETA1-6 : angle 1.46120 ( 3) SS BOND : bond 0.00330 ( 6) SS BOND : angle 1.44398 ( 12) covalent geometry : bond 0.00374 ( 6081) covalent geometry : angle 0.66304 ( 8316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7630 (mmt-90) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.3233 time to fit residues: 54.9293 Evaluate side-chains 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.195482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166379 restraints weight = 23002.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173800 restraints weight = 10587.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.178204 restraints weight = 6478.125| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6097 Z= 0.168 Angle : 0.589 5.765 8358 Z= 0.306 Chirality : 0.039 0.192 990 Planarity : 0.005 0.085 1016 Dihedral : 8.415 62.512 1080 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 7.18 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 754 helix: 2.01 (0.25), residues: 416 sheet: 0.23 (0.75), residues: 52 loop : 0.11 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.003 0.001 HIS B 112 PHE 0.012 0.001 PHE B 222 TYR 0.018 0.001 TYR B 153 ARG 0.004 0.001 ARG A 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 4) link_NAG-ASN : angle 2.40891 ( 12) link_BETA1-4 : bond 0.00920 ( 4) link_BETA1-4 : angle 2.04194 ( 12) link_ALPHA1-3 : bond 0.00833 ( 1) link_ALPHA1-3 : angle 3.03818 ( 3) hydrogen bonds : bond 0.05048 ( 368) hydrogen bonds : angle 4.92566 ( 1047) link_BETA1-6 : bond 0.00019 ( 1) link_BETA1-6 : angle 1.50132 ( 3) SS BOND : bond 0.00563 ( 6) SS BOND : angle 1.04615 ( 12) covalent geometry : bond 0.00361 ( 6081) covalent geometry : angle 0.57362 ( 8316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7780 (mmt-90) outliers start: 8 outliers final: 6 residues processed: 112 average time/residue: 0.4227 time to fit residues: 65.7689 Evaluate side-chains 108 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160961 restraints weight = 23423.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168361 restraints weight = 10473.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172962 restraints weight = 6344.664| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6097 Z= 0.145 Angle : 0.553 5.929 8358 Z= 0.282 Chirality : 0.038 0.217 990 Planarity : 0.004 0.063 1016 Dihedral : 6.648 55.041 1080 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.79 % Allowed : 7.67 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.32), residues: 754 helix: 2.16 (0.26), residues: 420 sheet: 0.26 (0.77), residues: 52 loop : 0.12 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.005 0.001 HIS B 55 PHE 0.011 0.001 PHE A 295 TYR 0.018 0.001 TYR B 153 ARG 0.004 0.001 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 4) link_NAG-ASN : angle 2.10914 ( 12) link_BETA1-4 : bond 0.00711 ( 4) link_BETA1-4 : angle 1.81726 ( 12) link_ALPHA1-3 : bond 0.01138 ( 1) link_ALPHA1-3 : angle 2.75452 ( 3) hydrogen bonds : bond 0.04524 ( 368) hydrogen bonds : angle 4.56462 ( 1047) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.30131 ( 3) SS BOND : bond 0.00401 ( 6) SS BOND : angle 0.82647 ( 12) covalent geometry : bond 0.00318 ( 6081) covalent geometry : angle 0.53997 ( 8316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7890 (mmt-90) REVERT: A 360 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6227 (mm-30) REVERT: A 540 TRP cc_start: 0.7269 (t60) cc_final: 0.6670 (t60) REVERT: B 166 ASP cc_start: 0.7970 (t0) cc_final: 0.7744 (t70) outliers start: 11 outliers final: 8 residues processed: 114 average time/residue: 0.3635 time to fit residues: 56.3137 Evaluate side-chains 106 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159001 restraints weight = 23257.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166170 restraints weight = 10589.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.170637 restraints weight = 6491.911| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6097 Z= 0.146 Angle : 0.548 6.808 8358 Z= 0.278 Chirality : 0.038 0.213 990 Planarity : 0.004 0.056 1016 Dihedral : 6.115 55.790 1080 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.79 % Allowed : 8.48 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.31), residues: 754 helix: 2.34 (0.26), residues: 420 sheet: 0.14 (0.72), residues: 55 loop : 0.09 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 520 HIS 0.003 0.001 HIS B 55 PHE 0.011 0.001 PHE A 295 TYR 0.019 0.001 TYR B 153 ARG 0.003 0.000 ARG A 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 4) link_NAG-ASN : angle 2.01205 ( 12) link_BETA1-4 : bond 0.00639 ( 4) link_BETA1-4 : angle 1.72011 ( 12) link_ALPHA1-3 : bond 0.00923 ( 1) link_ALPHA1-3 : angle 2.44142 ( 3) hydrogen bonds : bond 0.04221 ( 368) hydrogen bonds : angle 4.45193 ( 1047) link_BETA1-6 : bond 0.00167 ( 1) link_BETA1-6 : angle 1.38542 ( 3) SS BOND : bond 0.00553 ( 6) SS BOND : angle 1.49809 ( 12) covalent geometry : bond 0.00325 ( 6081) covalent geometry : angle 0.53471 ( 8316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7910 (mmt-90) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.3460 time to fit residues: 51.4388 Evaluate side-chains 106 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.184902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155730 restraints weight = 23278.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162847 restraints weight = 10729.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.167348 restraints weight = 6615.131| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6097 Z= 0.169 Angle : 0.557 6.081 8358 Z= 0.283 Chirality : 0.038 0.217 990 Planarity : 0.004 0.050 1016 Dihedral : 5.906 56.404 1080 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.94 % Allowed : 7.34 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.31), residues: 754 helix: 2.28 (0.25), residues: 425 sheet: 0.06 (0.73), residues: 55 loop : 0.12 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.004 0.001 HIS B 55 PHE 0.013 0.001 PHE A 295 TYR 0.014 0.001 TYR B 153 ARG 0.003 0.001 ARG A 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 4) link_NAG-ASN : angle 1.94453 ( 12) link_BETA1-4 : bond 0.00651 ( 4) link_BETA1-4 : angle 1.65206 ( 12) link_ALPHA1-3 : bond 0.00886 ( 1) link_ALPHA1-3 : angle 2.00230 ( 3) hydrogen bonds : bond 0.04251 ( 368) hydrogen bonds : angle 4.42898 ( 1047) link_BETA1-6 : bond 0.00199 ( 1) link_BETA1-6 : angle 1.35896 ( 3) SS BOND : bond 0.00383 ( 6) SS BOND : angle 1.16208 ( 12) covalent geometry : bond 0.00373 ( 6081) covalent geometry : angle 0.54629 ( 8316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7945 (mmt-90) outliers start: 18 outliers final: 14 residues processed: 113 average time/residue: 0.3412 time to fit residues: 52.2783 Evaluate side-chains 107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156564 restraints weight = 23225.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163802 restraints weight = 10555.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168344 restraints weight = 6479.739| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6097 Z= 0.126 Angle : 0.534 6.045 8358 Z= 0.270 Chirality : 0.037 0.220 990 Planarity : 0.004 0.045 1016 Dihedral : 5.629 56.466 1080 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.77 % Allowed : 8.65 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.31), residues: 754 helix: 2.55 (0.25), residues: 418 sheet: 0.03 (0.74), residues: 55 loop : 0.16 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.004 0.001 HIS B 55 PHE 0.011 0.001 PHE A 295 TYR 0.016 0.001 TYR B 153 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 4) link_NAG-ASN : angle 1.85039 ( 12) link_BETA1-4 : bond 0.00708 ( 4) link_BETA1-4 : angle 1.65511 ( 12) link_ALPHA1-3 : bond 0.00947 ( 1) link_ALPHA1-3 : angle 1.64915 ( 3) hydrogen bonds : bond 0.04041 ( 368) hydrogen bonds : angle 4.32870 ( 1047) link_BETA1-6 : bond 0.00237 ( 1) link_BETA1-6 : angle 1.32286 ( 3) SS BOND : bond 0.00425 ( 6) SS BOND : angle 1.12531 ( 12) covalent geometry : bond 0.00282 ( 6081) covalent geometry : angle 0.52407 ( 8316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7963 (mmt-90) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.3711 time to fit residues: 54.9863 Evaluate side-chains 107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.184839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155637 restraints weight = 23365.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162851 restraints weight = 10625.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167387 restraints weight = 6532.903| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6097 Z= 0.139 Angle : 0.538 6.209 8358 Z= 0.272 Chirality : 0.037 0.219 990 Planarity : 0.004 0.044 1016 Dihedral : 5.528 56.673 1080 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.94 % Allowed : 8.48 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.32), residues: 754 helix: 2.66 (0.26), residues: 414 sheet: -0.35 (0.70), residues: 61 loop : 0.11 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 520 HIS 0.005 0.001 HIS B 125 PHE 0.011 0.001 PHE A 111 TYR 0.016 0.001 TYR B 153 ARG 0.001 0.000 ARG A 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 4) link_NAG-ASN : angle 1.77898 ( 12) link_BETA1-4 : bond 0.00692 ( 4) link_BETA1-4 : angle 1.61918 ( 12) link_ALPHA1-3 : bond 0.00871 ( 1) link_ALPHA1-3 : angle 1.59225 ( 3) hydrogen bonds : bond 0.04049 ( 368) hydrogen bonds : angle 4.30452 ( 1047) link_BETA1-6 : bond 0.00215 ( 1) link_BETA1-6 : angle 1.33652 ( 3) SS BOND : bond 0.00296 ( 6) SS BOND : angle 1.03701 ( 12) covalent geometry : bond 0.00315 ( 6081) covalent geometry : angle 0.52830 ( 8316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8372 (m-10) cc_final: 0.8083 (m-10) REVERT: A 351 MET cc_start: 0.8070 (ttp) cc_final: 0.7841 (ttp) REVERT: A 353 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7966 (mmt-90) REVERT: B 59 GLU cc_start: 0.8312 (pm20) cc_final: 0.8064 (pm20) outliers start: 18 outliers final: 14 residues processed: 105 average time/residue: 0.3551 time to fit residues: 50.4017 Evaluate side-chains 104 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144903 restraints weight = 22715.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151465 restraints weight = 10448.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155633 restraints weight = 6442.292| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6097 Z= 0.137 Angle : 0.538 5.961 8358 Z= 0.271 Chirality : 0.038 0.224 990 Planarity : 0.004 0.044 1016 Dihedral : 5.434 56.655 1080 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.77 % Allowed : 8.65 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.32), residues: 754 helix: 2.71 (0.26), residues: 413 sheet: -0.39 (0.69), residues: 61 loop : 0.15 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 520 HIS 0.003 0.001 HIS B 55 PHE 0.011 0.001 PHE A 111 TYR 0.016 0.001 TYR B 153 ARG 0.004 0.000 ARG B 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 4) link_NAG-ASN : angle 1.73632 ( 12) link_BETA1-4 : bond 0.00711 ( 4) link_BETA1-4 : angle 1.59177 ( 12) link_ALPHA1-3 : bond 0.00874 ( 1) link_ALPHA1-3 : angle 1.45978 ( 3) hydrogen bonds : bond 0.03985 ( 368) hydrogen bonds : angle 4.25885 ( 1047) link_BETA1-6 : bond 0.00225 ( 1) link_BETA1-6 : angle 1.33513 ( 3) SS BOND : bond 0.00351 ( 6) SS BOND : angle 0.90981 ( 12) covalent geometry : bond 0.00310 ( 6081) covalent geometry : angle 0.52967 ( 8316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8314 (m-10) cc_final: 0.8077 (m-10) REVERT: A 351 MET cc_start: 0.8090 (ttp) cc_final: 0.7886 (ttp) REVERT: A 353 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7969 (mmt-90) outliers start: 17 outliers final: 15 residues processed: 105 average time/residue: 0.3663 time to fit residues: 51.8492 Evaluate side-chains 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.0000 chunk 49 optimal weight: 0.3980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147382 restraints weight = 22637.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153714 restraints weight = 10686.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157785 restraints weight = 6658.418| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6097 Z= 0.109 Angle : 0.525 6.011 8358 Z= 0.263 Chirality : 0.037 0.222 990 Planarity : 0.004 0.041 1016 Dihedral : 5.214 56.411 1080 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.12 % Allowed : 9.14 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.32), residues: 754 helix: 2.81 (0.26), residues: 413 sheet: -0.36 (0.70), residues: 61 loop : 0.23 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 520 HIS 0.003 0.001 HIS B 55 PHE 0.009 0.001 PHE A 295 TYR 0.015 0.001 TYR B 153 ARG 0.002 0.000 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 4) link_NAG-ASN : angle 1.62407 ( 12) link_BETA1-4 : bond 0.00778 ( 4) link_BETA1-4 : angle 1.60850 ( 12) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 1.26703 ( 3) hydrogen bonds : bond 0.03840 ( 368) hydrogen bonds : angle 4.16580 ( 1047) link_BETA1-6 : bond 0.00103 ( 1) link_BETA1-6 : angle 1.22173 ( 3) SS BOND : bond 0.00337 ( 6) SS BOND : angle 0.80182 ( 12) covalent geometry : bond 0.00245 ( 6081) covalent geometry : angle 0.51726 ( 8316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8249 (m-10) cc_final: 0.8016 (m-10) REVERT: A 233 VAL cc_start: 0.8960 (m) cc_final: 0.8596 (p) REVERT: B 59 GLU cc_start: 0.8298 (pm20) cc_final: 0.8053 (pm20) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.3767 time to fit residues: 51.2019 Evaluate side-chains 107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144792 restraints weight = 22845.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150994 restraints weight = 11010.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154954 restraints weight = 6949.973| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6097 Z= 0.176 Angle : 0.565 6.179 8358 Z= 0.288 Chirality : 0.038 0.222 990 Planarity : 0.004 0.058 1016 Dihedral : 5.509 56.578 1080 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.28 % Allowed : 9.14 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.32), residues: 754 helix: 2.69 (0.26), residues: 413 sheet: -0.43 (0.71), residues: 62 loop : 0.12 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 520 HIS 0.003 0.001 HIS B 55 PHE 0.017 0.001 PHE A 111 TYR 0.033 0.002 TYR A 593 ARG 0.003 0.001 ARG A 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 4) link_NAG-ASN : angle 1.61920 ( 12) link_BETA1-4 : bond 0.00714 ( 4) link_BETA1-4 : angle 1.56925 ( 12) link_ALPHA1-3 : bond 0.00761 ( 1) link_ALPHA1-3 : angle 1.63151 ( 3) hydrogen bonds : bond 0.04121 ( 368) hydrogen bonds : angle 4.31261 ( 1047) link_BETA1-6 : bond 0.00183 ( 1) link_BETA1-6 : angle 1.37672 ( 3) SS BOND : bond 0.00404 ( 6) SS BOND : angle 0.96245 ( 12) covalent geometry : bond 0.00410 ( 6081) covalent geometry : angle 0.55744 ( 8316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 46 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8293 (m-10) cc_final: 0.8055 (m-10) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.3383 time to fit residues: 45.7361 Evaluate side-chains 104 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143612 restraints weight = 22513.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149845 restraints weight = 11006.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153847 restraints weight = 6962.099| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6097 Z= 0.129 Angle : 0.536 6.067 8358 Z= 0.270 Chirality : 0.037 0.234 990 Planarity : 0.004 0.042 1016 Dihedral : 5.350 56.192 1080 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.45 % Allowed : 9.14 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.32), residues: 754 helix: 2.78 (0.26), residues: 413 sheet: -0.45 (0.71), residues: 62 loop : 0.21 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 520 HIS 0.003 0.001 HIS B 55 PHE 0.011 0.001 PHE A 111 TYR 0.015 0.001 TYR A 593 ARG 0.001 0.000 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 1.61509 ( 12) link_BETA1-4 : bond 0.00762 ( 4) link_BETA1-4 : angle 1.59211 ( 12) link_ALPHA1-3 : bond 0.00901 ( 1) link_ALPHA1-3 : angle 1.30588 ( 3) hydrogen bonds : bond 0.03936 ( 368) hydrogen bonds : angle 4.21308 ( 1047) link_BETA1-6 : bond 0.00230 ( 1) link_BETA1-6 : angle 1.33911 ( 3) SS BOND : bond 0.00352 ( 6) SS BOND : angle 0.71949 ( 12) covalent geometry : bond 0.00294 ( 6081) covalent geometry : angle 0.52854 ( 8316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4366.40 seconds wall clock time: 76 minutes 17.58 seconds (4577.58 seconds total)